GENOME DATABASES

The Cytochrome P450 Homepage

David R. Nelson*
Department of Molecular Sciences, University of Tennessee, 858 Madison Avenue, Memphis, TN 38163, USA
*Correspondence to: Tel: þ1 901 448 8303; Fax: þ1 901 448 7360; E-mail: [email protected]

Date received (in revised form): 21st August 2009

Abstract
The Cytochrome P450 Homepage is a universal resource for nomenclature and sequence information on cyto-
chrome P450 (CYP) genes. The site has been in continuous operation since February 1995. Currently, naming
information for 11,512 CYPs are available on the web pages. The P450 sequences are manually curated by David
Nelson, and the nomenclature system conforms to an evolutionary scheme such that members of CYP families
and subfamilies share common ancestors. The organisation and content of the Homepage are described.

Keywords: cytochrome P450, annotation, hand curation, protein family databases

History of the Cytochrome P450 The Cytochrome P450 Homepage was started
on a desktop Macintosh Quadra 650, running
Homepage WebStar as the server software. I believe MOSAIC
The Homepage (http://drnelson.utmem.edu/ was the web browser at that time. The 1993 paper
CytochromeP450.html) grew out of a need for had 221 P450 genes and 12 pseudogenes listed.1
unlimited space to present nomenclature and On 10th October, 1995 I gave a talk at the Third
annotation information on cytochrome P450 International Symposium on Cytochrome P450
sequences. The 1993 cytochrome P450 nomen- Biodiversity in Woods Hole, Massachusetts, titled:
clature paper1 was 51 pages long and was the last ‘450 Cytochrome P450s’, so the number of CYPs
dedicated P450 nomenclature publication before had doubled in less than two years. I posted a
the website was opened in February 1995. That sequence alignment on a wall at that meeting with
paper had 12 authors, all well known in the field. all the non-confidential P450s. This occupied
Multi-author agreement was the strategy of Daniel about a 2  3 metre squared space, and everyone
W. Nebert, who with Frank J. Gonzalez launched wanted to come to see their own sequences.
the standardised cytochrome P450 nomenclature Clearly, publications could not include such
system in 1987,2 with follow-ups in 19893 and large alignments, and there was no space to discuss
1991.4 The P450 nomenclature prior to this individual sequences. Even 51-page papers could
system was fragmented and difficult, with many only include long tables to list the genes. A website
laboratories having their own shorthand notation was the solution. The initial web pages were very
for P450s, often based on molecular weight or simple lists of html code showing entries by CYP
migration position on gels. For example, CYP2A1 name in alpha-numeric order. The purpose was to
had six different names in the literature. The new include the 200þ new sequences that were not in
CYP nomenclature was one of the first systematic the 1993 paper. This was stated at the top of the
nomenclatures for a protein superfamily and it nomenclature pages as: ‘P450s that have appeared
became adopted for use by many other groups since the 1993 P450 nomenclature update’. At that
struggling with the rapid expansion of sequence time, entering 200 sequence names, accessions,
data in the 1980s. references and percentage identity information

# HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO 1. 59 – 65 OCTOBER 2009 59
GENOME DATABASES Nelson

seemed like a large task. Today, a single plant smaller. Even so, the files are getting to be fairly
genome may have over 300 CYP genes, and if you large. Part C is 685 html text pages. The nomen-
include pseudogenes, over 400 CYPs. The soybean clature has CYP numbers reserved, as shown in
genome has 332 full-length CYP genes and 368 Table 1. Original plans were for 100 CYP families
pseudogenes for a total of 700 CYP sequences. only, but this was a gross underestimate. We had to
go to three-digit CYP names and now we are using
four-digit CYP names for bacteria and lower eukar-
Organisation of the Homepage yotes. This required the first reserved blocks of
The Homepage has grown over time. A format was numbers to be multiplied by ten and then 100 to
chosen to allow easy expansion and rapid access to continue the numbering. Four of the five files are
the parts you most wanted to visit. The first page specific for animals (Part A, Part B), plants (Part D)
of the website is the main access point (Figure 1) and bacteria (Part E). Part C covers families —
and it serves as a visual sitemap. The coloured box CYP10– 69, CYP301– 699 and CYP3001–
at the top marked P450 WEB MATRIX is a link 6999 — which include both animals and lower
to another page with P450-related sites. Some of eukaryotes. This may need separation in the future.
these sites are dedicated to specific groups of There are three families that occur in more than
species, like insects, plants or fungi, and they may one group. CYP51 is found in all kingdoms: plants,
include expression data, phylogenetic trees and animals, lower eukaryotes and bacteria, although
other features. Below the WEB MATRIX box is a there are species that do not have CYP51. CYP51
link to a description of how to search the site using was the first fungal P450 sequence identified from
Google. This may allow the discovery of things that Saccharomyces cerevisiae. Therefore, it has a lower eukar-
are not obvious from the table layout. The next yote number. CYP97 is found in plants and some
section is the main table. At the top there are four lower eukaryotes like diatoms. It was first described in
rows with general links. The most important of Arabidopsis, so it has a plant CYP number. CYP701 is
these is the nomenclature link, which takes you to also found in plants and lower eukaryotes, including
a page with links to five main bibliographic files choanoflagellates, the ancestors of animals. This family
that include the CYP nomenclature entries. These is orthologous to fungal CYP61. CYP51, CYP61 and
are broken into sections to keep the file sizes CYP701 are found in sterol biosynthesis pathways.

Figure 1. The top of Cytochrome P450 Homepage.

60 # HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO. 1. 59 –65 OCTOBER 2009
The Cytochrome P450 Homepage GENOME DATABASES

Table 1. CYP numbering scheme name for the given species or group. The files on
Animals Plants Lower the server have not been updated recently, but
eukaryotes more current sequences have been added to this
page. The files: ‘All bacterial P450s’ and ‘All fungal
1–49 71 –99 51–69
(CYP49A2) (CYP99A12) (CYP69A1) P450s’ are new. Plans are in progress to revamp the
P450 Blast server to include all 11,512 named P450
300 –499 701 –999 501– 699
sequences. Currently, there are no single files that
(CYP379A3) (CYP804A1) (CYP699A2)
contain all the animal (3,282 sequences), plant
3001–4999 7001–9999 5001–6999 (4,266 sequences) or protist (247 sequences) P450s;
(reserved) (reserved) (CYP5314A1*) however, many of these sequences are available on
Bacteria the appropriate species pages.
The three-dimensional P450 structure tour was
101 –299 (CYP299A1)
constructed using Protein Explorer, which depends
1001–2999 (CYP1015A1) on a CHIME plug-in. The newer Netscape and
Numbers in parentheses are the last assigned CYP name in that block.
*An unusual group of hybrid fungal P450s are given the block 6001 –6099 (6004A2) so
Firefox browsers do not support the CHIME
that they can be kept together. plug-in, so this page is difficult to view as it was
intended to be. It does run perfectly well on a Mac
Navigation inside the nomenclature files can be G4 OS 9.1 with Netscape Communicator 4.7 as
accomplished by bookmarks to specific locations. the browser, the CHIME plug-in installed and the
These are links found at the top of the file. These mime-type chemical/x-pdb added to the accepted
links will jump you to the family or subfamily indi- mime types in the browser preferences. There are
cated. You can use a browser find command at any still places to download old versions of Netscape
time. This will take you to the next occurrence of (http://browser.netscape.com/releases) for the
a word or name in the file. You can use the back determined P450 afficionado. The structure tour
button to return to the nomenclature index page has 37 views of CYP101A1 and CYP2C5 P450
or the main page. structure, emphasising various features around the
The link marked ‘databases’ in row one is an molecule, including salt bridges, interactions of side
effort to make the data more accessible. The chains with the haem propionates, the PERF
Cytochrome P450 Homepage is not a relational motif, etc. I am not currently planning to convert
database and it suffers from the drawbacks of a long this tour to a more user-friendly version.
text file that contains the information. These data- The P450 genomes page (row two) lists com-
base files were intended to bring information on pleted genomes and the number of P450s found in
individual CYP subfamilies into a format where each. This page has not been updated and will need
they could be easily accessed, with links to the considerable revision. The fungal genomes page
sequence data, phylogenetic trees and the nomen- (http://drnelson.utmem.edu/fungal.genomes.html)
clature pages all in one table each for plants, now includes 55 complete fungal genomes, with
animals, lower eukaryotes and bacteria/archaea. links to the named P450 sequences for each species.
The idea is good but little data entry has occurred In 1995, when the Homepage was started, I
in these files, as the pressure to name more and created a directory of P450 researchers, with e-mail
more genes has pushed these other aspects of the addresses and pictures if I could find them. This is
Homepage into lower priority status. called the Rogue’s Gallery. There is a picture of the
On the second row of the main table there is a very young author in these pages. Although many
link to P450 BLAST server sequences. These are of the links are no longer functional, these pages
files of CYP sequences that are searchable by are being updated as time permits.
BLAST on the P450 BLAST server (http://blast. The P450 statistics page on row four has infor-
uthsc.edu). These sequences are presented by CYP mation on how many P450s are named in the

# HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO 1. 59 – 65 OCTOBER 2009 61
GENOME DATABASES Nelson

various sections: plant, animal, fungi, protist and have links to the MedLine abstract. Often the
bacteria. The older versions from previous years are high-profile genome papers in Science and Nature
included. This page has links to some useful spread- are free of charge at the publisher’s site. Next to the
sheets that contain all the known CYP names. publications page is the P450 Talks/Lectures page.
Most of these are in CYP name order, but a few Here are found the transcripts and PowerPoint pre-
new ones have been sorted by species. There are sentations of 14 lectures I have given since 2000.
August 2009 files for all P450s from plants, animals, The text has indications of slide numbers
insects, fungi, protists and bacteria. These files were embedded, so one can easily follow along with the
used to count the P450s after subtracting the var- PowerPoint presentation. Some of the older lectures
iants (usually indicated by v1, v2 etc after the CYP have the slides inserted in the text. There is also a
name). The P450 counts do include pseudogenes. 2009 version of a medical school introductory
Table 2 shows the current P450 statistics. lecture on human P450s.
Several links, such as ‘What’s New’, ‘Trees’ and
‘Alignments’, are self explanatory. The ‘What’s New’
page is not updated very often, even though many
The species pages
additions and revisions to the Homepage are being The rest of the main table is divided into four sec-
made frequently. The ‘Trees’ and ‘Alignments’ pages tions: animals, plants, lower eukaryotes and bac-
are also pretty old files. More comprehensive sets of teria. The lower eukaryotes section is subdivided
alignments and trees can be found at the into additional sections and fungi have been given
Cytochrome P450 Engineering Database5 (http:// a whole page of their own, due to the recent
www.cyped.uni-stuttgart.de/). More trees showing sequencing of nearly 100 species of fungi. Clicking
fungal P450 clans can be found on the fungal P450 on a species link will take you to a species page,
page. Additional trees are linked from inside the where sequence data annotation information and
database’s pages. more links will be available. The best way to
The publications page has been updated to explore the Homepage is to click on links and read
include papers from 2009. Many of the older the annotations at the tops of the files.
papers have links to pdf files. The newer papers

Animals
Table 2. Named P450 sequences (19th August, 2009) Human and mouse are the most extensively anno-
tated of the animal CYPs.6 I have made master
Animals 3,282
tables with links to a wide variety of data for these
two species. Links to the master tables are found on
Insects 1,675 (part of the animal total) the mouse and human species pages. The human
Animals 1,607 master table contains more than 700 links to
(not human P450 data. There are ten columns of data
insects) in the human table (Figure 2). These include links
Plants 4,266 to protein, mRNA, genomic DNA, Online
Mendelian Inheritance in Man (OMIM), HUGO
Fungi 2,784
Gene Nomenclature Committee (HGNC),
Protists 247 Unigene and Entrez Gene entries, plus three-
Bacteria 905 dimensional structures, including the recent aroma-
tase CYP19 structure. Column one also has links to
Archaea 26
seven manually created gene cluster maps. This
Viruses 2 (Mimivirus) table is at the mercy of the other databases that are
Total 11,512 linked. In 2007, all the HGNC data links looked

62 # HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO. 1. 59 –65 OCTOBER 2009
The Cytochrome P450 Homepage GENOME DATABASES

like http://www.gene.ucl.uk/nomenclature/data/ D. pseudoobscura page. Unique information on

get_data.php?hgnc_id=nnnn, but in 2009 they all our D. pseudoobscura page includes a sequence align-
look like http://www.genenames.org/data/hgnc_ ment with all the intron locations colour coded for
data.php?hgnc_id=nnnn. Therefore, 141 links to phase. There is also a discussion of intron gain and
the HGNC had to be changed in the table. The loss. The Fungal Cytochrome P450 Database8 in
mouse master table is very similar but it does not Korea is beginning to include animal data. The
contain OMIM or HGNC data columns. The sequences from the 12 Drosophila species are
mouse table has links to the UCSC browser included on the website (http://p450.riceblast.snu.
(column 6), which shows the vicinity of the CYP ac.kr/index.php?a=view).
genes. From the mouse species page, a tree is avail- Species pages include the dates of the last major
able that includes 103 mouse and 60 human revision. The animal pages have dates from 2003 to
sequences. Orthologue pairs are shown in red. 2008. Pages may be updated at any time. For
Each species page was created separately and con- example, the zebrafish page will soon be updated,
tains different information in addition to sequence since a paper on the Danio rerio genome CYPs is in
data. Drosophila melanogaster is another highly preparation. Some pages are placeholders for data that
studied animal. There is a dedicated P450 site that have not yet been processed. Elephant shark, lamprey
includes several insect species, including Drosophila. and Acropora (a coral) are examples. Some of these,
(http://p450.sophia.inra.fr/), which is linked at the such as sponge, are awaiting genome papers to be
top of the D. melanogaster species page. I highly rec- released before the sequence data can be made public.
ommend it. There are now 12 species of Drosophila
that have been sequenced.7 Our site has only ana-
lysed two: D. melanogaster and D. pseudoobscura. The Plants
D. pseudoobscura page has both species’ P450s side Plants have many more P450s than animals. The
by side for easy comparison, with D. melanogaster in soybean has about six times more CYP genes than
blue and D. pseudoobscura in red. A tree with 169 the human — and that only counts full genes.
Drosophila sequences included is linked from the Because of the larger number of genes, and the

Figure 2. The top part of the Human P450 Master Table.

# HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO 1. 59 – 65 OCTOBER 2009 63
GENOME DATABASES Nelson

emphasis on animals, not many plant genomes have five oomyctes (stramenopiles) and Leishmania infan-
yet been sequenced. Other plant genomes, such as tum (Euglenozoa) (http://p450.riceblast.snu.ac.kr/
pine and ferns, have been deferred because the index.php?a=view). These data are obtained from
genomes are huge and too expensive to sequence at an automated pipeline designed to find P450s from
the moment. Papers have been published compar- genomic data. The method is rapid and very good
ing CYPs from Arabidopsis and rice;9 these two plus at finding P450s. Many of the gene assemblies
Chlamydomonas, poplar and moss;10 and comparing found by this automated method are very short
CYPs from six completed plant genomes, including fragments, however, often missing exons and/or
papaya and grape.11 Arabidopsis has other sites dedi- splicing the exons together at incorrect locations.
cated to CYPs in Denmark (http://www.p450.kvl. The authors have attempted to assign P450 families
dk/) and The University of Illinois at Urbana- based on a comparison with the manually curated
Champaign (http://arabidopsis-p450.biotec.uiuc. sequences at the Cytochrome P450 Homepage.
edu/). The Arabidopsis Information Resource site The process is very useful for surveying a genome
(TAIR) also contains P450 data (http://www.arabi- for P450s, but manual curation is needed in the
dopsis.org/). end to achieve a more accurate gene assembly. So
Genome sequencing centres such as the Broad far, I have processed 55 fungal genomes, three oomy-
Institute and the Joint Genome Institute ( JGI) have cete genomes and six Euglenozoa genomes. These
their own genome browsers to access data from their P450s are on my website, with CYP names assigned
projects. The cottonwood Populus trichocarpa was after manual annotation of the sequences. The
sequenced at JGI. My P. trichocarpa page has a Korean Fungal Cytochrome P450 Database contains
detailed tutorial on how to use the JGI browser. 32 fungal genomes that had not been entered into
This tutorial is applicable to any of the genomes at the Cytochrome P450 Homepage as of 16th August,
JGI. Recently, a plant genome browser called 2009. These genomes have 3,471 predicted P450s in
Phytozome 4.0 was released (http://www.phyto- them, so the Homepage site, with 2,784 named
zome.net/). This is like the University of California, fungal P450s, is not up to date, but, ultimately, hand
Santa Cruz (UCSC) browser for animals except that curation produces more accurate gene assemblies.
it has 14 complete plant genomes included. One can Other sites, such as the Fungal Cytochrome P450
search for P450 as a keyword against 20 nodes on a Database8 and the Cytochrome P450 Engineering
schematic phylogeny of the plant genomes. As an Database,5 depend on the systematic nomenclature
example, a search of the rice/Brachypodium distachyon found on the Homepage to predict family or subfam-
clade identified 309 P450 gene clusters that presum- ily membership for new sequences.
ably contain orthologues or clusters of closely related
genes. Our rice page has a file showing the com-
parison of rice and Arabidopsis CYPs with gene Other lower eukaryotes and Mimivirus
names in a side-by-side table format (http://drnel- Below ‘fungi’ in the main table is a collection of
son.utmem.edu/rice.arab.list.htm). protist P450s. These organisms are eukaryotes that
A more comprehensive table with six plant are not plants, animals or fungi, so they are very
species is included as Supplementary Table 2 to diverse. Aside from CYP51 and CYP710, these
Nelson10 (http://drnelson.utmem.edu/Nelson.Supp organisms do not share CYP families with other
FigsandTables.pdf). eukaryotes. A complete list of the 247 CYPs in a
spreadsheet format is available under the ‘P450 Stats’
Fungi link. The sequences are accessible from the species
Fungal genome sequences have been accumulating pages. The large virus called Mimivirus has two
rapidly. The dedicated Korean Fungal Cytochrome CYPs, CYP5253A1 and CYP5254A1.12 The origin
P450 Database8 has P450s from 87 species of fungi, of these CYPs is unclear, but they may have been

64 # HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO. 1. 59 –65 OCTOBER 2009
The Cytochrome P450 Homepage GENOME DATABASES

picked up from an amoeba host, so they are included orthologues with the same name, is already begin-
in the CYP numbers reserved for lower eukaryotes. ning to simplify the nomenclature. There is a need
for a deeper time nomenclature that recognises very
Bacteria deep time clades of P450s. This is the clan nomen-
The last link in the main table is to bacteria. This clature, and there will be more about this nomencla-
also includes the 26 named ‘Archaeal CYPs’. Some ture on the Homepage in the future, as it becomes
bacteria in the Actinobacteria have 18 to over 30 more fully developed. Of great significance for this
CYPs (Streptomyces species and Mycobacterium Homepage is a mechanism for funding the work.
species), while most other bacteria tend to have Even though this nomenclature system is 22 years
only a few or none. Because bacteria generally have old, and this website is 14 years old, no grant has
few P450s, there are no bacterial species pages. The ever been given specifically for this annotation
CYPs are presented in name order. P450s in effort. This is probably not sustainable, yet annotation
bacteria are often associated with antibiotic bio- is fundamental to progress in genomics. Funding
synthesis. As an interesting aside, the first analysis agencies need to realise the essential nature of gene
of the Sorcerer II Global Ocean Sampling annotation by funding nomenclature efforts.
expedition13 identified 3,305 CYPs from marine
bacteria. These have not been named.
References
Links below the main table
1. Nelson, D.R., Kamataki, T., Waxman, D.J., Guengerich, F.P. et al.
The Cytochrome P450 Homepage is visited by (1993), ‘The P450 superfamily: Update on new sequences, gene
mapping, accession numbers, early trivial names of enzymes and nomen-
many P450 researchers, so links have been provided clature’, DNA Cell Biol. Vol. 12, pp. 1– 51.
to P450-related meetings. These appear below the 2. Nebert, D.W. and Gonzalez, F.J. (1987), ‘P450 genes: Structure, evol-
ution, and regulation’, Annu. Rev. Biochem. Vol. 56, pp. 945– 993.
main table. Many of the old meeting links still 3. Nebert, D.W., Nelson, D.R., Adesnik, M.A., Coon, M.J. et al. (1989),
work. There are also some links to other P450 ‘The P450 superfamily: Update on listing of all genes and recommended
nomenclature of the chromosomal loci. DNA Vol. 8, pp. 1– 13.
sites, although these have mostly been moved to 4. Nebert, D.W., Nelson, D.R., Coon, M.J., Estabrook, R.W. et al. (1991),
the P450 WEB MATRIX table. The old links have ‘The P450 superfamily: Update on new sequences, gene mapping and
recommended nomenclature’, DNA Cell Biol. Vol. 10, pp. 1– 14.
not been removed, so this is more or less a histori- 5. Fischer, M., Knoll, M., Sirim, D., Wagner, F. et al. (2007), ‘The Cytochrome
cal list. P450 Engineering Database: A navigation and prediction tool for the cyto-
chrome P450 protein family’, Bioinformatics Vol. 23, pp. 2015–2017.
6. Nelson, D.R., Zeldin, D.C., Hoffman, S.M.G., Maltais, L. et al. (2004),
Future plans ‘Comparison of cytochrome P450 (CYP) genes from the mouse and
human genomes including nomenclature recommendations for genes, pseu-
The Homepage is primarily a nomenclature site. dogenes, and alternative-splice variants’, Pharmacogenetics Vol. 14, pp. 1–18.
7. Drosophila 12 Genomes Consortium (2007), ‘Evolution of genes and
It has run on a desktop computer in my office genomes on the Drosophila phylogeny’, Nature Vol. 450, pp. 203–218.
for 14 years, but it needs a long-term permanent 8. Park, J., Lee, S., Choi, J., Ahn, K. et al. (2008), ‘Fungal cytochrome
P450 database’, BMC Genomics Vol. 9, p. 402.
home, possibly with the National Center for 9. Nelson, D.R., Schuler, M.A., Paquette, S.M., Werck-Reichhart, D. et al.
Biotechnology Information (NCBI) or some other (2004), ‘Comparative genomics of Oryza sativa and Arabidopsis thaliana.
Analysis of 727 cytochrome P450 genes and pseudogenes from a
established sequence repository. Once the nomen- monocot and a dicot’, Plant Physiol. Vol. 135, pp. 756– 772.
clature has saturated a phylum such that no new 10. Nelson, D.R. (2006), ‘Plant cytochrome P450s from moss to poplar’,
Phytochem. Rev. Vol. 5, pp. 193–204.
families are being discovered, it may not be necess- 11. Nelson, D.R., Ming, R., Alam, M. and Schuler, M.A. (2008),
ary to continue to name every sequence from every ‘Comparison of cytochrome P450 genes from six plant genomes’, Tropical
Plant Biology Vol. 1, pp. 216–235.
species. The recent sequencing of numerous mam- 12. Lamb, D.C., Lei, L., Warrilow, A.G., Lepesheva, G.I. et al. (2009), ‘The
malian genomes has shown that all mammalian, and first virally encoded cytochrome p450’, J. Virol. Vol. 83, pp. 8266– 8269.
13. Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L. et al. (2007), ‘The
possibly all vertebrate, CYP families have been Sorcerer II Global Ocean Sampling expedition: Expanding the universe
found. Orthologue identification, and naming of protein families’, PLoS Biol. 5, p. e16.

# HENRY STEWART PUBLICATIONS 1479 –7364. HUMAN GENOMICS. VOL 4. NO 1. 59 – 65 OCTOBER 2009 65